def runProgram(program, params):
""" Runs a em program setting its environment matching a prefix"""
env = None
# Allow passing absolute paths
programName = basename(program)
from pwem import Domain
# Avoid detecting xmipp installation script to be run as xmipp, since
# it will run devel installation with production xmippEnv.json environment:
# Example: want to compile devel with java 8, but production was compiled with java 11.
# So java 11 makes it into the PATH taking priority
if programName.startswith('xmipp_'):
print("Xmipp command detected")
xmipp3 = Domain.getPlugin('xmipp3').Plugin
env = xmipp3.getEnviron()
if programName.startswith('relion'):
print("relion command detected")
relion = Domain.getPlugin("relion").Plugin
env = relion.getEnviron()
elif (programName.startswith('e2') or programName.startswith('sx')):
print("eman/sparx command detected")
eman2 = Domain.importFromPlugin('eman2', 'Plugin')
env = eman2.getEnviron()
elif programName.startswith('b'):
print("Bsoft command detected")
bsoft = Domain.importFromPlugin('bsoft', 'Plugin')
env = bsoft.getEnviron()
pwutils.runJob(None, program, params, env=env)
def runProgram(program, params):
""" Runs a em program setting its environment matching a prefix"""
env = None
# Allow passing absolute paths
programName = basename(program)
from pwem import Domain
if programName.startswith('xmipp'):
xmipp3 = Domain.getPlugin('xmipp3').Plugin
env = xmipp3.getEnviron()
if programName.startswith('relion'):
relion = Domain.getPlugin("relion").Plugin
env = relion.getEnviron()
print(env)
elif (programName.startswith('e2') or programName.startswith('sx')):
eman2 = Domain.importFromPlugin('eman2', 'Plugin')
env = eman2.getEnviron()
elif programName.startswith('b'):
bsoft = Domain.importFromPlugin('bsoft', 'Plugin')
env = bsoft.getEnviron()
pwutils.runJob(None, program, params, env=env)
def test_plugin(self):
# Really stupid test to check that tomo plugin is defined
tomo = Domain.getPlugin('tomo')
self.assertFalse(tomo is None)
self.assertTrue(hasattr(tomo, 'Plugin'))
# Check that defined objects here are found
objects = Domain.getObjects()
expected = [
'TiltImage', 'TiltSeries', 'SetOfTiltSeries', 'TiltImageM',
'TiltSeriesM', 'SetOfTiltSeriesM'
]
for e in expected:
self.assertTrue(e in objects,
"%s should be in Domain.getObjects" % e)
print("Objects")
pwutils.prettyDict(Domain.getObjects())
print("Protocols")
pwutils.prettyDict(Domain.getProtocols())
print("Viewers")
pwutils.prettyDict(Domain.getViewers())
elif n == 2:
if sys.argv[1] in ['-h', '--help', 'help']:
usage()
pluginName = sys.argv[1]
plugin = Domain.getPlugin(pluginName)
print("Plugin: %s" % pluginName)
for subName in [
'constants', 'convert', 'protocols', 'wizards', 'viewers', 'tests'
]:
sub, error = getSubmodule(plugin, pluginName, subName)
if sub is None:
if error is None:
msg = " missing"
else:
exitWithErrors = True
msg = " error -> %s" % error
else:
msg = " loaded"